DNA Overview: how Next Generation Sequencing is revolutionising Kennedy DNA testing! (November 2017 rewrite)


My Y chromosome position 12,790,481 (hg38) showing the G->A transition that marks M222!

27.11.2017 rewrite.

This page covers phase 2 of my Kennedy DNA study, historical notes on phase 1 and some haplogroup notes about my own Y chromosome group (M222, FGC4077 and FGC5856), and finally some remarks on the ever popular autosomal tests.

Kennedy DNA study Phase 2 (2013-2017+)

The seeds for phase 2 were probably sown in 2012 with the publication of the citizen science paper by Rocca et al. on mass SNP discovery and Dr. J Wilson's sequencing of two R-M222 males, resulting in the breakthrough 2013 SNP array test called 'Chromo2'. This affordable test for the first time enabled surname projects to switch over to a SNP-first approach. Chromo2 was rapidly overtaken by more flexible SNP test panels developed by Dr. T. Krahn, one of Rocca's co-authors, made available via his 'YSEQ' lab in Berlin. The advantage of the SNP/next-generation sequencing method is simply that the rates of false positives are virtually zero - in fact since 2013 there has not been a single false positive in the Kennedy project. Depending on budget and whether funding is coming from the project, testing usually involves the YSEQ lab for single and fixed panel SNP testing and Full Genomes Inc. for the more advanced sequencing (sometimes loosely referred to as 'SNP discovery' testing). Most of the branches studied during Phase 1 have now been retested using SNP testing methods, as well as using the latter for new samples. With SNP results it is much easier to draw unambiguous 'trees' (cladograms) showing the exact relationships of all the Kennedy branches. The R-M222 part of the overall Kennedy results tree is public on this site and shares results with general M222 men due to surname-haplogroup collaboration efforts (see the M222 secton below). All the Scottish and Ulster branch discoveries were made by my project. Dr. Thomas Krahn identified the core marker for the Tipperary ('Dalcassian') O'Kennedys in 2009.

The project will cover the costs of testing if a male Kennedy is available with a proven paper trail to a rural parish in Scotland or Ireland. Men not qualifying under those conditions are of course more than welcome to test under direction of the project.

IMPORTANT: ALL KENNEDY BRANCHES (SNPs, HAPLOGROUPS) ARE OF EQUAL INTEREST TO THE PROJECT!!

Kennedy DNA study Phase 1 (2004-2012)

The depracated Y-STR testing method was commercialized back in 2000, using techniques explored by academics Dr. Bryan Sykes and Dr. Mark Thomas. Their papers on the Sykes surname and the Cohanim priesthood set the scene for what ultimately turned out to be a flawed matching system which in some instances could have 'false positive' rates exceeding 90%. My own Y-STR testing commenced in 2004 and from 2006 to early 2013 I tested considerable numbers of male Kennedys using this method. This data now has to be considered obsolete.

The M222, FGC4077 and FGC5856 haplogroups (2006-2017+)

I was a first day tester of the M222 SNP in early 2006 when Drs. James Wilson and David Faux first put it on sale at the sadly missed Ethnoancestry lab. Because of this I divide my time between the Kennedy surname project and M222 research - of course my interest grows as I near my own sub-branch M222-FGC4077 and then FGC5856. Kennedys occur in no less than EIGHT sub-branches of M222. This is why I publish a joint chart of M222 and Kennedy data. This tree extends upwards and sideways but the non-M222 sections are not online at the time of writing. The chart is on pdf format and can be text searched for surnames of interest eg Kennedy!

So what exactly is this chart? Originally it was designed as a CHROMO2 RESULTS TRACKER. Therefore the tree it started off with was of course the Dr. Wilson M222 tree published during the rollout of Chromo2. Within weeks my own sequencing data had determined that FGC4077 was the branch accounting for most of the unassigned testers on Chromo2 and so this branch was added to the tree. As I identified new branches these and the test surnames were also added. At all times branches were only added after I had proven them to my satisfaction based on raw data. Apart from the original Wilson markers (which numbered around 24) it was my own work and not copied from anyone else's tree. This research continued until mid-2015 when I reduced my direct work and started to rely more on the analysis work of YFull.com who do professional BAM data analysis. I co-admin the YFull M222 project with Aidan Byrne. A review of the history of M222 research from 1999 onwards can be read here.

Following my own sequencing and the discovery that the FGC4077 branch represented in excess of 10% of all M222 men, informal group discussions led to a suggestion to create a mailing list which was set up by Gerry Hoy, I act as the admin/moderator. Results are shared via my M222 chart and the YFull R-Y3454 tree their name for the group). This group covers everything at or below FGC4077, FGC4078, FGC4087, A725, FGC12948, FGC5856 and M4491 sub-branches and so on below. If you have a positive result for one of these, please contact me to join the group.

The M222 SNP chart including the M222 Kennedys is here.

I almost forgot - what about Autosomal testing?!

In the last few years affordable tests from Ancestry.com and 23andMe have become household names and have taken over the bulk of the market share. Both have multi-million sized databases with Ancestry recently announcing they had tested 6 million men and women. Most of the markers they test are on the autosomes chromosomes 1 to 22. Confusingly though, they do have a small selection of X and Y chromosome markers as well as mitochondrial (mtDNA) markers. Although they have improved they are not comparable with the detailed and very current Y SNP test panels from YSEQ. The tests are hence good for finding close cousins on all tree branches but poor for deep examination of male kindreds. I continue to urge takers of these two tests to get their raw data uploaded to the comparison site GEDMatch (or Genesis-GEDMatch for the latest 23andMe test). If you are a Kennedy, drop me a line with your GEDMatch kit number. We can then discuss whether the raw data contains any Y SNP markers of use.

For further information please contact the project.